Magnesium in PDB 8ugs: Cryo-Em Structure of Bovine Phosphodiesterase 6 Bound to Cgmp

All present enzymatic activity of Cryo-Em Structure of Bovine Phosphodiesterase 6 Bound to Cgmp:
3.1.4.35;

The structure of Cryo-Em Structure of Bovine Phosphodiesterase 6 Bound to Cgmp also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium atom in the Cryo-Em Structure of Bovine Phosphodiesterase 6 Bound to Cgmp (pdb code 8ugs). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Cryo-Em Structure of Bovine Phosphodiesterase 6 Bound to Cgmp, PDB code: 8ugs:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Cryo-Em Structure of Bovine Phosphodiesterase 6 Bound to Cgmp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Em Structure of Bovine Phosphodiesterase 6 Bound to Cgmp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg903 b:33.9 occ:1.00 O1A A:PCG904 2.1 85.0 1.0 OD1 A:ASP600 2.6 58.6 1.0 PA A:PCG904 3.5 92.2 1.0 CG A:ASP600 3.5 57.9 1.0 OD2 A:ASP600 3.7 51.3 1.0 OE2 A:GLU628 3.9 81.6 1.0 O5' A:PCG904 3.9 86.3 1.0 O2A A:PCG904 4.0 84.7 1.0 ZN A:ZN902 4.2 93.1 1.0 CD2 A:HIS631 4.4 49.5 1.0 OD2 A:ASP720 4.4 86.7 1.0 CD2 A:HIS599 4.5 52.9 1.0 O A:HIS599 4.5 68.4 1.0 NE2 A:HIS631 4.5 54.1 1.0 CD A:GLU628 4.5 74.8 1.0 CG2 A:THR669 4.5 63.3 1.0 CD2 A:HIS603 4.6 56.0 1.0 NE2 A:HIS603 4.6 56.9 1.0 CG A:GLU628 4.6 64.4 1.0 O3' A:PCG904 4.8 89.6 1.0 CB A:ASP600 4.9 54.0 1.0 CD2 A:HIS559 5.0 68.3 1.0

Magnesium binding site 2 out of 2 in the Cryo-Em Structure of Bovine Phosphodiesterase 6 Bound to Cgmp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryo-Em Structure of Bovine Phosphodiesterase 6 Bound to Cgmp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg903 b:20.4 occ:1.00 O1A B:PCG904 2.0 80.8 1.0 OD1 B:ASP598 2.3 63.0 1.0 CG B:ASP598 3.3 64.9 1.0 OD2 B:ASP598 3.5 67.3 1.0 PA B:PCG904 3.6 88.7 1.0 CE1 B:HIS597 3.8 78.9 1.0 O B:HIS597 4.1 65.8 1.0 ZN B:ZN902 4.1 141.3 1.0 O2A B:PCG904 4.1 83.0 1.0 CD2 B:HIS629 4.2 48.3 1.0 NE2 B:HIS629 4.2 51.1 1.0 ND1 B:HIS597 4.3 78.9 1.0 O5' B:PCG904 4.3 71.2 1.0 OE2 B:GLU626 4.4 74.5 1.0 OG1 B:THR667 4.4 64.0 1.0 CD2 B:HIS601 4.5 53.8 1.0 CB B:ASP598 4.6 51.1 1.0 NE2 B:HIS597 4.6 74.2 1.0 O3' B:PCG904 4.7 85.0 1.0 CD B:GLU626 4.7 69.3 1.0 CG B:GLU626 4.7 61.6 1.0 NE2 B:HIS601 4.8 56.7 1.0 CB B:THR667 4.9 53.7 1.0 OD2 B:ASP718 4.9 77.0 1.0 CA B:ASP598 4.9 51.6 1.0

C.Aplin, R.A.Cerione. Probing the Mechanism By Which the Retinal G Protein Transducin Activates Its Biological Effector PDE6. J.Biol.Chem. 05608 2023.
ISSN: ESSN 1083-351X
PubMed: 38159849
DOI: 10.1016/J.JBC.2023.105608